Literature DB >> 30848458

Leveraging Big Data to Transform Drug Discovery.

Benjamin S Glicksberg1,2, Li Li2,3, Rong Chen2,3, Joel Dudley2, Bin Chen4,5,6.   

Abstract

The surge of public disease and drug-related data availability has facilitated the application of computational methodologies to transform drug discovery. In the current chapter, we outline and detail the various resources and tools one can leverage in order to perform such analyses. We further describe in depth the in silico workflows of two recent studies that have identified possible novel indications of existing drugs. Lastly, we delve into the caveats and considerations of this process to enable other researchers to perform rigorous computational drug discovery experiments of their own.

Entities:  

Keywords:  Big data; Bioinformatics; Clinical informatics; Drug discovery; Drug repositioning; Drug repurposing; Electronic medical records; Gene expression data; Pharmacogenomics; Systems pharmacology

Mesh:

Year:  2019        PMID: 30848458      PMCID: PMC6657335          DOI: 10.1007/978-1-4939-9089-4_6

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  72 in total

1.  Significance analysis of microarrays applied to the ionizing radiation response.

Authors:  V G Tusher; R Tibshirani; G Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-17       Impact factor: 11.205

2.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Authors:  Ron Edgar; Michael Domrachev; Alex E Lash
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  The Unified Medical Language System (UMLS): integrating biomedical terminology.

Authors:  Olivier Bodenreider
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  Drug target validation: Hitting the target.

Authors:  Caitlin Smith
Journal:  Nature       Date:  2003-03-20       Impact factor: 49.962

5.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

Review 6.  Drug repositioning: identifying and developing new uses for existing drugs.

Authors:  Ted T Ashburn; Karl B Thor
Journal:  Nat Rev Drug Discov       Date:  2004-08       Impact factor: 84.694

7.  External validity of randomised controlled trials: "to whom do the results of this trial apply?".

Authors:  Peter M Rothwell
Journal:  Lancet       Date:  2005 Jan 1-7       Impact factor: 79.321

8.  Treating expression levels of different genes as a sample in microarray data analysis: is it worth a risk?

Authors:  Lev Klebanov; Andrei Yakovlev
Journal:  Stat Appl Genet Mol Biol       Date:  2006-03-24

9.  Participation in cancer clinical trials: race-, sex-, and age-based disparities.

Authors:  Vivek H Murthy; Harlan M Krumholz; Cary P Gross
Journal:  JAMA       Date:  2004-06-09       Impact factor: 56.272

10.  DrugBank: a comprehensive resource for in silico drug discovery and exploration.

Authors:  David S Wishart; Craig Knox; An Chi Guo; Savita Shrivastava; Murtaza Hassanali; Paul Stothard; Zhan Chang; Jennifer Woolsey
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

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  3 in total

1.  OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features.

Authors:  Billy Zeng; Benjamin S Glicksberg; Patrick Newbury; Evgeny Chekalin; Jing Xing; Ke Liu; Anita Wen; Caven Chow; Bin Chen
Journal:  Nat Protoc       Date:  2020-12-23       Impact factor: 13.491

Review 2.  Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system.

Authors:  Vertika Gautam; Anand Gaurav; Neeraj Masand; Vannajan Sanghiran Lee; Vaishali M Patil
Journal:  Mol Divers       Date:  2022-07-11       Impact factor: 3.364

Review 3.  Genome-wide Signatures of Early-Life Stress: Influence of Sex.

Authors:  Sero Toriano Parel; Catherine Jensen Peña
Journal:  Biol Psychiatry       Date:  2020-12-19       Impact factor: 13.382

  3 in total

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